Kemri finds Africa's first fungus resistant to major drugs in Nairobi patient

A swab was taken from the wound and grown in the laboratory.

Researchers have found in Nairobi a notorious fungus that resisted all four major classes of antifungal medicines tested, making it the first such case documented in Africa and only the second in the world.

The fungus, called Candidozyma auris, formerly Candida auris, was found in a 28-year-old woman who developed an infection at a surgical wound while being treated at a tertiary hospital in the city.

Researchers from the Kenya Medical Research Institute (Kemri) and the Walter Reed Army Institute of Research-Africa, who reported the finding, said this is concerning because C. auris is already known to spread easily in hospitals and can colonise patients for long periods.

It can cause serious infections of wounds, the bloodstream and urinary tract. It can also spread from one part of the body into the blood and become life-threatening.

The World Health Organization has classified C. auris as a critical priority fungal pathogen because of its drug resistance and its potential to spread. Some studies estimate a mortality rate of 30 per cent to 53 per cent of patients affected by an invasive infection.

"Pan-drug-resistant (PDR) isolates, resistant to four antifungal classes, are exceedingly rare, previously reported from a single patient in New York, US (2022). We report phenotypic and genomic features of a PDR C. auris isolate from Kenya, the second globally," the researchers wrote.

They called this an alarming threat in places with few treatment options.

 Their report, titled "Emergence of pan-drug resistant Candidozyma auris in Kenya, the second globally documented case", was published online on September 29 in the journal Scientific Reports.

C. Auris is one of the world's most feared hospital microbes.

The Kenyan woman underwent elective surgery last year but later developed a hospital-acquired infection at the surgical site, with pus.

The woman received multiple antibiotics and antifungal drugs over eight months, from February to October.

When her fever did not clear, a swab was taken from the wound and was grown in the laboratory.

Tests showed the isolate resisted fluconazole, caspofungin, micafungin, amphotericin B and flucytosine. These medicines belong to four major groups of antifungal drugs.

A fifth drug, voriconazole, was also measured, but the researchers could not interpret the result because no official cut-off exists.

The team also read the fungus's DNA using whole-genome sequencing. They found several genetic changes already linked to resistance, and two mutations they describe as new.

The researchers say the resistance may have developed independently in Kenya, although they cannot establish exactly how it arose.

They could also not rule out the possibility that it was brought into Kenya from an unsampled source.

"Clinically, the emergence of a PDR C. auris in Kenya poses a substantial threat to patient care, particularly in resource-limited settings where novel antifungal agents such as ibrexafungerp are not widely available," they said.

The researchers called for robust surveillance, rapid diagnostic capacity and strict antifungal stewardship to prevent further spread of drug-resistant pathogens.

“These findings underscore the critical importance of robust antifungal stewardship, infection prevention, and rapid diagnostic capacity to mitigate the spread of highly resistant C. auris lineages in healthcare settings," they said.

"Continued expansion of C. auris surveillance across Kenyan healthcare facilities will be important for defining its epidemiology, transmission dynamics, antifungal resistance and genetic diversity."

The authors include Erick Odoyo, Collins Kigen, James Wachira, Vanessa Natasha, Stephen Ondolo, Martin Georges and Allan Wataka. Others are Luis Pow Sang, Robert C Haynes and Lillian Musila. The US Army health surveillance programme funded the work.

Drug-resistant infections are already a serious problem in Kenya. The Institute for Health Metrics and Evaluation estimated that about 6,670 deaths in Kenya in 2021 were associated with antimicrobial resistance, meaning resistance contributed to the deaths.

The Kemri-Wellcome Trust Research Programme says countries like Kenya suffer disproportionately because they have restricted access to third- and fourth-line drugs, the medicines given when standard treatment fails.

A recent four-year study of children admitted to a national referral hospital found that 73 of the 113 deaths among children with resistant infections were attributable to the resistance.